X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FEditCommand.java;h=ba66e82727398b8ff73572ed650f4ad3f1ce937f;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=019e11eb4e2de0d9849d1ad56056976a25980e4e;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git
diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 019e11e..ba66e82 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -1,20 +1,20 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.commands;
@@ -56,6 +56,8 @@ public class EditCommand implements CommandI
public static final int REPLACE = 4;
+ public static final int INSERT_NUC = 5;
+
Edit[] edits;
String description;
@@ -95,11 +97,13 @@ public class EditCommand implements CommandI
performEdit(0, null);
}
+ @Override
final public String getDescription()
{
return description;
}
+ @Override
public int getSize()
{
return edits == null ? 0 : edits.length;
@@ -144,8 +148,8 @@ public class EditCommand implements CommandI
final public void appendEdit(int command, SequenceI[] seqs, int position,
int number, AlignmentI al, boolean performEdit, AlignmentI[] views)
{
- Edit edit = new Edit(command, seqs, position, number, al
- .getGapCharacter());
+ Edit edit = new Edit(command, seqs, position, number,
+ al.getGapCharacter());
if (al.getHeight() == seqs.length)
{
edit.al = al;
@@ -193,15 +197,21 @@ public class EditCommand implements CommandI
case REPLACE:
replace(edits[e]);
break;
+ // TODO:add deleteNuc for UNDO
+ // case INSERT_NUC:
+ // insertNuc(edits[e]);
+ // break;
}
}
}
+ @Override
final public void doCommand(AlignmentI[] views)
{
performEdit(0, views);
}
+ @Override
final public void undoCommand(AlignmentI[] views)
{
int e = 0, eSize = edits.length;
@@ -235,11 +245,25 @@ public class EditCommand implements CommandI
{
command.seqs[s].insertCharAt(command.position, command.number,
command.gapChar);
+ // System.out.println("pos: "+command.position+" number: "+command.number);
}
adjustAnnotations(command, true, false, null);
}
+ //
+ // final void insertNuc(Edit command)
+ // {
+ //
+ // for (int s = 0; s < command.seqs.length; s++)
+ // {
+ // System.out.println("pos: "+command.position+" number: "+command.number);
+ // command.seqs[s].insertCharAt(command.position, command.number,'A');
+ // }
+ //
+ // adjustAnnotations(command, true, false, null);
+ // }
+
final void deleteGap(Edit command)
{
for (int s = 0; s < command.seqs.length; s++)
@@ -287,9 +311,12 @@ public class EditCommand implements CommandI
command.oldds = new SequenceI[command.seqs.length];
}
command.oldds[i] = oldds;
- adjustFeatures(command, i, command.seqs[i]
- .findPosition(command.position), command.seqs[i]
- .findPosition(command.position + command.number), false);
+ adjustFeatures(
+ command,
+ i,
+ command.seqs[i].findPosition(command.position),
+ command.seqs[i].findPosition(command.position
+ + command.number), false);
}
}
}
@@ -323,8 +350,11 @@ public class EditCommand implements CommandI
// read it to the alignment
if (command.alIndex[i] < command.al.getHeight())
{
- command.al.getSequences().insertElementAt(command.seqs[i],
- command.alIndex[i]);
+ List sequences;
+ synchronized (sequences = command.al.getSequences())
+ {
+ sequences.add(command.alIndex[i], command.seqs[i]);
+ }
}
else
{
@@ -425,6 +455,9 @@ public class EditCommand implements CommandI
command.number = start + command.string[0].length;
for (int i = 0; i < command.seqs.length; i++)
{
+ boolean newDSWasNeeded = command.oldds != null
+ && command.oldds[i] != null;
+
/**
* cut addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT,
* cut, sg.getStartRes(), sg.getEndRes()-sg.getStartRes()+1,
@@ -439,9 +472,48 @@ public class EditCommand implements CommandI
oldstring = command.seqs[i].getSequenceAsString();
tmp = new StringBuffer(oldstring.substring(0, start));
tmp.append(command.string[i]);
+ String nogaprep = jalview.analysis.AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars, new String(
+ command.string[i]));
+ int ipos = command.seqs[i].findPosition(start)
+ - command.seqs[i].getStart();
tmp.append(oldstring.substring(end));
command.seqs[i].setSequence(tmp.toString());
command.string[i] = oldstring.substring(start, end).toCharArray();
+ String nogapold = jalview.analysis.AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars, new String(
+ command.string[i]));
+ if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase()))
+ {
+ if (newDSWasNeeded)
+ {
+ SequenceI oldds = command.seqs[i].getDatasetSequence();
+ command.seqs[i].setDatasetSequence(command.oldds[i]);
+ command.oldds[i] = oldds;
+ }
+ else
+ {
+ if (command.oldds == null)
+ {
+ command.oldds = new SequenceI[command.seqs.length];
+ }
+ command.oldds[i] = command.seqs[i].getDatasetSequence();
+ SequenceI newds = new Sequence(
+ command.seqs[i].getDatasetSequence());
+ String fullseq, osp = newds.getSequenceAsString();
+ fullseq = osp.substring(0, ipos) + nogaprep
+ + osp.substring(ipos + nogaprep.length());
+ newds.setSequence(fullseq.toUpperCase());
+ // TODO: JAL-1131 ensure newly created dataset sequence is added to
+ // the set of
+ // dataset sequences associated with the alignment.
+ // TODO: JAL-1131 fix up any annotation associated with new dataset
+ // sequence to ensure that original sequence/annotation relationships
+ // are preserved.
+ command.seqs[i].setDatasetSequence(newds);
+
+ }
+ }
tmp = null;
oldstring = null;
}
@@ -782,9 +854,8 @@ public class EditCommand implements CommandI
if (command.editedFeatures != null
&& command.editedFeatures.containsKey(seq))
{
- sequence
- .setSequenceFeatures((SequenceFeature[]) command.editedFeatures
- .get(seq));
+ sequence.setSequenceFeatures((SequenceFeature[]) command.editedFeatures
+ .get(seq));
}
return;